Interpretive Summary: Theobroma cacao, the source of cocoa beans for chocolate, is an important tropical agriculture commodity that is affected by a number of fungal pathogens and insect pests, as well as concerns about yield and quality. We are trying to find molecular genetic markers that are linked to disease resistance and other important economic traits to aid in a marker assisted selection (MAS) breeding program for cacao to ensure a reliable supply of cocoa for the US confectionary industry. Currently there are about 500 molecular genetic markers for cacao and we are taking advantage of the cacao genome sequencing project to expand that to greater than 50,000 single-nucleotide polymorphism (SNP) markers. We will use these markers to improve the resolution of our current genetic maps and to find associations between specific SNPs and advantageous traits such as disease resistance or higher yield. By studying linkage disequilibrium in cacao populations, we can determine how close to the gene that controls the trait our markers have to be. Our results are important to scientists trying to understand the mechanism of disease resistance and, eventually, to cacao farmers who will benefit from superior disease resistant and more productive cultivars produced through our MAS breeding program.

Technical Abstract:
Although the potential of Linkage Disequilibrium (LD) mapping to associate markers to agronomic and horticultural traits has been already recognized in cacao, its real efficiency depends on the nature and structure of the LD in the genome of the populations under study. LD is dependent on several factors, such as recombination, mutation, migration, selection, mating system, and genetic drift. However, only the LD caused by recombination is useful for mapping purposes. Selection, genetic drift and mating system, will cause spurious association between markers and scored traits within populations undergoing such processes. Recently, a study of the genetic diversity of cacao reported an important amount of differentiation, potentially caused by genetic drift, among the cacao genetic groups and populations. Knowing the amount and the structure of the LD in these populations will greatly facilitate future association mapping studies to identify markers linked to traits of agronomic interest in cacao. In this paper we show the amount and structure of linkage disequilibrium and the degree of linkage disequilibrium decay among 93 microsatellite markers distributed across the 10 cacao linkage groups at an average of 9.83 cM. Six cultivated and natural cacao populations were analyzed for this study. An important proportion of the linkage disequilibrium found was caused by spurious associations among markers and its consequence is discussed for planning future association mapping platforms.